Characterisation and profiling of Bacillus subtilis,Bacillus cereus and Bacillus licheniformis by MALDI-TOF mass fingerprinting

The Bacillus genus includes species such as Bacillus cereus, Bacillus licheniformis and Bacillus subtilis, some of which may be pathogenic or causative agents in the spoilage of food products. The main goal of this work was to apply matrix-assisted laser desorption ionisation-time of flight (MALDI-TOF) mass fingerprinting to the classification of these Bacillus species. Genetic analyses were also compared to phyloproteomic analyses. A collection of 57 Bacillus strains isolated from fresh and processed food and from culture collections were studied and their mass spectra compiled. The resulting mass fingerprints were compared and characteristic peaks at the strain and species levels were assigned. The results showed that MALDI-TOF was a good complementary approach to 16S rRNA sequencing and even a more powerful tool in the accurate classification of Bacillus species, especially for differentiating B. subtilis and B. cereus from Bacillus amyloliquefaciens and Bacillus thuringiensis, respectively. MALDI-TOF was also found to provide valuable information at both intra- and interspecies levels in the Bacillus species studied.     

Detection and quantification of spoilage and pathogenic Bacillus cereus, Bacillus subtilis and Bacillus licheniformis by real-time PCR

A new primer-probe set for the detection and quantification of Bacillus cereus, Bacillus licheniformis and Bacillus subtilis by real-time PCR (Rti-PCR) was developed. For it, forty-eight strains belonging to these species were considered. The DNA of these strains was isolated and a fragment of the 16S rRNA gene amplified. The amplicons were sequenced and the obtained sequences were aligned with reference sequences from the GenBank. For the development of the Real-Time PCR (RTi-PCR) methodology based on TaqMan probes, a primer pair and probe, specific for the studied Bacillus spp., were designed. To establish the quantification method, two RTi-PCR standard curves were constructed; one with DNA extracted from a serially-diluted B. cereus culture and a second curve with DNA extracted from a sterilised food product inoculated with serial dilutions of B. cereus. The curves exhibited R² values of 0.9969 and 0.9958 respectively. Linear correlations between the log₁₀ input DNA concentration and the threshold cycle (Ct) values were observed with a magnitude of linearity in the range of 1.65 × 10¹ CFU/mL to 1.65 × 10⁶ CFU/mL for both standard curves. The specificity of the designed primers and probe was tested with DNA extracted from B. cereus, B. licheniformis and B. subtilis strains, which gave Ct values between 14 and 15, whereas non-specific amplifications of the DNA from other microbial species of food interest exhibited a Ct value above 28.5. To our knowledge, this method represents the first study about the quantification of spoilage and/or pathogenic B. cereus, B. licheniformis and B. subtilis in food products, with the aim to prevent the presence of these undesirable species in the food chain.     

Role of mechanical vs. chemical action in the removal of adherent Bacillus spores during CIP procedures

This study was designed to evaluate the respective roles of mechanical and chemical effects on the removal of Bacillus spores during cleaning-in-place. This analysis was performed on 12 strains belonging to the Bacillus cereus group (B. cereus, Bacillus anthracis, Bacillus thuringiensis) or to less related Bacillus species (Bacillus pumilus, Bacillus licheniformis, Bacillus sporothermodurans, Bacillus subtilis). Adherent spores were subjected to rinsing-in-place (mechanical action) and cleaning-in-place (mechanical and chemical actions) procedures, the latter involving NaOH 0.5% at 60 °C. Results revealed that mechanical action alone only removed between 53 and 89% of the attached spores at a shear stress of 500 Pa. This resistance to shear was not related to spore surface properties. Conversely, in the presence of NaOH at a shear stress of 4 Pa, spores were readily detached, with between 80 and 99% of the adherent spores detached during CIP and the chemical action greatly depended on the strain. This finding suggests that chemical action plays the major role during CIP, whose efficacy is significantly governed by the spore surface chemistry.     

Inactivation of Bacillus cereus spores using a combined treatment of UV-TiO2 photocatalysis and high hydrostatic pressure

Bacillus cereus spores are resistant to high hydrostatic pressure (HHP) processing treatment. A combination of UV-TiO₂ photocatalysis (UVTP for 10 min) and two cycles of 600 MPa HHP treatment for 10 min for the first cycle and 1 min for the second cycle (UVTP-2HHP) at ambient temperature was applied to inactivate B. cereus spores inoculated on a solidified agar matrix (SAM) used as a model matrix. Two cycles of HHP treatment were used as a strategy for induction of spore germination, followed by inactivation. UVTP and 2 cycles of HHP resulted in a 5.0-log CFU/cm² spore reduction (initial spore count was 6.6 log CFU/cm²), including an approximate 0.8-log CFU/cm² reduction due to a synergistic effect. The inactivation mechanism of UVTP pretreatment was related to lipid peroxidation of the spore membrane based on the level of malondialdehyde (MDA) making spores susceptible to the HHP treatment. Flow cytometry and transmission electron microscopic (TEM) analyses showed severe physiological alteration and structural damage to spores after the combined treatment. UVTP and 2 cycles of HHP showed potential for effective inactivation of B. cereus to ensure food safety from B. cereus spores on food products.Practical applicationsInactivation of bacterial spores remains a technical challenge for HHP and other interventions because spores are highly resistant to high pressure. Pretreatment with UVTP followed by two cycles of HHP resulted in reduction in B. cereus spores due to a synergistic effect. This hurdle technology of UVTP and HHP can help food industry in ensuring food safety against the Bacillus spores.     

The detection of viable vegetative cells of Bacillus sporothermodurans using propidium monoazide with semi-nested PCR

Bacillus sporothermodurans produces highly heat-resistant spores that can survive ultra-high temperature (UHT) treatment in milk. Therefore, we developed a rapid, specific and sensitive semi-nested touchdown PCR assay combined with propidium monoazide (PMA) treatment for the detection of viable B. sporothermodurans vegetative cells. The semi-nested touchdown PCR alone proved to be specific for B. sporothermodurans, and the achieved detection limit was 4 CFU/mL from bacterial culture and artificially contaminated UHT milk. This method combined with PMA treatment was shown to amplify DNA specifically from viable cells and presented a detection limit of 10² CFU/mL in UHT milk. The developed PMA-PCR assay shows applicability for the specific detection of viable cells of B. sporothermodurans from UHT milk. This method is of special significance for applications in the food industry by reducing the time required for the analysis of milk and dairy products for the presence of this microorganism.     

Pressure–ohmic–thermal sterilization: A feasible approach for the inactivation of Bacillus amyloliquefaciens and Geobacillus stearothermophilus spores

The efficacy of a pressure–ohmic–thermal sterilization (POTS) for Bacillus amyloliquefaciens and Geobacillus stearothermophilus spore inactivation was investigated. Spores (2.5 × 10⁸ cfu/ml) were inoculated in 0.1% NaCl solution (pH 5.0 and 7.0), green pea puree (pH 6.1), carrot puree (pH 5.0) or tomato juice (pH 4.1). Samples were ohmically (50 V/cm) treated at 600 MPa and 105 °C for various holding times using a laboratory-scale high-pressure processor. B. amyloliquefaciens and G. stearothermophilus spores suspended in 0.1% NaCl solution (pH 7.0) were inactivated by 4.6 and 5.6 log, respectively, for a 30-min holding time. B. amyloliquefaciens and G. stearothermophilus spores in tomato juice were reduced by 3.1 and 4.8 log, respectively, for a 10-min holding time. Spore germination was highest in the G. stearothermophilus suspended in 0.1% NaCl solution (pH 7.0). POTS treatment appears to be a potent method for inactivating pressure–thermal resistant bacterial spores.Industrial RelevanceFood industry is interested in developing superior quality low-acid shelf-stable foods. This study evaluated the pressure–ohmic–thermal sterilization (POTS) for the inactivation of Bacillus amyloliquefaciens and Bacillus stearothermophilus endospores. The impact of food matrices and acidity on the spore resistance was also investigated. Knowledge gained from the study will help the food processors for understanding the importance of various POTS treatment parameters for sterilization of low-acid foods.     

Microbial and physiochemical properties of Cheonggukjang fermented using Bacillus strains with antibacterial or antifungal activities

Cheonggukjang was produced with improved functionalities and safety using Bacillus subtilis W42 with an antibacterial activity and B. amyloliquefaciens MJ1-4 with an antifungal activity as starters with coinoculation of B. subtilis W42 and B. amyloliquefaciens (MW Cheonggukjang). Control cheonggukjang was prepared by inoculation of B. subtilis 168 (BS cheonggukjang) or a commercial cheonggukjang prepared using traditional methods (TM cheonggukjang). Cheonggukjang samples were immediately spiked with B. cereus ATCC11778 (1×10⁵ CFU/g of dry soybean) and Penicillium sp. that produced ochratoxin (1×10⁵ spores/g of dry soybean). During 72 h of fermentation at 37°C, total Bacillus counts increased, reaching 10⁹ CFU/g in MW and BS cheonggukjang. Numbers of B. cereus and Penicillium sp. decreased. The largest reduction was observed in MW cheonggukjang. Fungi were not detected after 24 h in MW and BS cheonggukjang. Fibrinolytic activity was detected only from MW cheonggukjang and the antioxidant activity was highest in MW cheonggukjang.     

Magnetic nano-beads based separation combined with propidium monoazide treatment and multiplex PCR assay for simultaneous detection of viable Salmonella Typhimurium, Escherichia coli O157:H7 and Listeria monocytogenes in food products

We developed a rapid and reliable technique for simultaneous detection of Salmonella Typhimurium, Escherichia coli O157:H7 and Listeria monocytogenes that can be used in food products. Magnetic nano-beads (MNBs) based immunomagnetic separation (IMS) was used to separate the target bacterial cells while multiplex PCR (mPCR) was used to amplify the target genes. To detect only the viable bacteria, propidium monoazide (PMA) was applied to selectively suppress the DNA detection from dead cells. The results showed the detection limit of IMS-PMA-mPCR assay was about 10² CFU/ml (1.2 × 10² CFU/ml for S. Typhimurium, 4.0 × 10² CFU/ml for E. coli O157:H7 and 5.4 × 10² CFU/ml for L. monocytogenes) in pure culture and 10³ CFU/g (5.1 × 10³ CFU/g for S. Typhimurium, 7.5 × 10³ CFU/g for E. coli O157:H7 and 8.4 × 10³ CFU/g for L. monocytogenes) in spiking food products samples (lettuce, tomato and ground beef). This report has demonstrated for the first time, the effective use of rapid and reliable IMS combined with PMA treatment and mPCR assay for simultaneous detection of viable S. Typhimurium, E. coli O157:H7 and L. monocytogenes in spiked food samples. It is anticipated that the present approach will be applicable to simultaneous detection of the three target microorganisms for practical use.     

Microbiological assay with Bacillus licheniformis for the easy detection of quinolones in milk

This paper proposes a microbiological method in microtitre plates for the detection of residues of quinolones in milk. The method uses spores of Bacillus licheniformis in culture medium with a redox combination of indicators and gives a response time of 5.5 h. This method detects 92 μg L⁻¹ of ciprofloxacin, 63 μg L⁻¹ of danofloxacin, 109 μg L⁻¹ of enrofloxacin, 101 μg L⁻¹ of marbofloxacin and 109 μg L⁻¹ of sarafloxacin in milk. Therefore, the assay is easy to develop and to use in laboratory, allowing analysis of large numbers of samples at low cost. Due to its good sensitivity to quinolones, this assay can be used as a complementary test of commercial microbiological methods and thereby improve food security.     

Prevalence of Bacillus spp. in different food products collected in Argentina

The prevalence of Bacillus spp. in 279 samples of different food products collected in Argentina was studied. Bacillus spp. was confirmed in 28 out of 70 honey samples, 29 out of 29 flour samples, 15 out of 50 cheese samples, and 30 out of 30 spice samples, while Bacillus spp. was not found in fresh anchovy. Among the 70 honeys studied, Bacillus cereus, Bacillus pumilus, Bacillus laterosporus and Paenibacillus larvae subspp. larvae showed an incidence of 23%, 4%, 8% and 38%, respectively. More diversity of Bacillus species was found in rye flours than in white flours, Bacillus subtilis being the predominant species isolated from rye flour. B. cereus had an incidence of 50% in Port Salut Argentino cheeses. Meanwhile, B. pumilus was identified in both Port Salut and Quartirolo cheeses with an incidence of 50% and 25%, respectively. All the spices analysed showed Bacillus mycoides as the sole aerobic spore-forming bacilli isolated. The association of the presence of B. cereus, B. subtilis and Bacillus licheniformis with both the potential spoilage of foods and foodborne outbreaks is well known. In this study, Bacillus spp. had an incidence of 38% among all the samples analysed, therefore the monitoring of those species should be routinely done in microbiological food analyses.     

Inactivation of Bacillus spores in batch vs continuous heating systems at sterilisation temperatures

This study was performed to assess the heat resistance of spores of Bacillus species in batch and continuous heating systems under commercial sterilisation conditions. Spores of thermophilic Bacillus smithii and mesophilic Bacillus amyloliquefaciens were found to be highly heat resistant in the batch system. They were able to withstand typical sterilisation temperatures. B. amyloliquefaciens showed tailing in the batch system and, before the onset of the tailing, a higher inactivation rate than in the continuous system at low temperatures. The reason for the tailing might be the presence of spore aggregates which are disrupted in the continuous system.     

Development of a real-time PCR assay for detection and quantification of enterotoxigenic members of Bacillus cereus group in food samples

A highly sensitive real-time PCR (qPCR) procedure, targeting the phosphatidylcholine-specific phospholipase C gene (pc-plc), was developed for specific detection and quantification of strains belonging to Bacillus cereus group. The target region was selected based on the enterotoxigenic profiles of 75 Bacillus strains. The inclusivity and exclusivity of the RTi-PCR assay were assessed with 59 isolates of the B. cereus group, 16 other Bacillus spp., and 4 non-Bacillus strains. The assay was also used to construct calibration curves for different food matrices, and it had a wide quantification range of 6 log units using both serial dilutions of purified DNA and calibrated cell suspensions of B. cereus CECT 148^T. The detection limit for B. cereus in artificially contaminated liquid egg and reconstituted infant formula was about 3 CFU per reaction or 60 CFU/ml of food, with a relative accuracy of 86.27% to 116.12% in artificially contaminated liquid egg. Naturally contaminated food samples were tested for the presence of B. cereus with the standard method, a conventional PCR and the new developed RTi-PCR assay. Results showed that the new developed RTi-PCR assay is very suitable for detection and quantification of strains of B. cereus group in food samples without an enrichment step.     

A mixed-species microarray for identification of food spoilage bacilli

Failure of food preservation is frequently caused by thermostable spores of members of the Bacillaceae family, which show a wide spectrum of resistance to cleaning and preservation treatments. We constructed and validated a mixed-species genotyping array for 6 Bacillus species, including Bacillus subtilis, Bacillus licheniformis, Bacillus pumilus, Bacillus sporothermodurans, Bacillus cereus and Bacillus coagulans, and 4 Geobacillus species, including Geobacillus stearothermophilus, Geobacillus thermocatenulatus, Geobacillus toebii and Geobacillus sp., in order to track food spoilage isolates from ingredient to product. The discriminating power of the array was evaluated with sets of 42 reference and 20 test strains. Bacterial isolates contain a within-species-conserved core genome comprising 68-88% of the entire genome and a non-conserved accessory genome comprising 7-22%. The majority of the core genome markers do not hybridise between species, thus they allow for efficient discrimination at the species level. The accessory genome array markers provide high-resolution discrimination at the level of individual isolates from a single species. In conclusion, the reported mixed-species microarray contains discriminating markers that allow rapid and cost-effective typing of Bacillus food spoilage bacteria in a wide variety of food products.     

Identification and safety evaluation of Bacillus species occurring in high numbers during spontaneous fermentations to produce Gergoush, a traditional Sudanese bread snack

Gergoush is a naturally fermented Sudanese Bread snack produced in three fermentation steps (primary starter, adapted starter and final dough), followed by three baking steps for a half to one hour at above 200 °C. This study examines the microbiota of two sets of fermentations performed at a traditional production site in Khartoum, Sudan in 2006 and 2009, respectively. In 2006 four different milk/legume based primary starters (faba bean, chick pea, lentil and white bean) were sampled in order to enumerate and identify the Bacillus at species or group level. In 2009 specific focus was on the enumeration and safety evaluation of the dominant Bacillus cereus group species occurring during various Gergoush productions (including the three fermentations steps and after baking). In 2006, the primary starters contained Bacillus spp. in the order of between 7.7 and 8.1 log₁₀ CFU/g. Species identifications were performed by M13-PCR typing using the Escherichia coli phage M13 derived primer PM13 combined with internally transcribed 16-23S rRNA PCR, 16S rRNA gene and gyrA or gyrB gene sequencing, and selected phenotypic tests. Depending on the legume used, 40-68% of the isolates were identified as B. cereus sensu lato, 16-27% as Bacillus licheniformis, 8-32% as Bacillus subtilis and 4-20% as Bacillus sonorensis. During the second set of fermentation trials performed in 2009, the Bacillus spp. and B. cereus occurred in numbers of between 7.7-9.9 and 6.1-7.8 log₁₀ CFU/g, respectively, while no bacteria were detected after baking. A total of 180 B. cereus sensu lato isolates from four different primary starters, adapted starters and final doughs were further identified as B. cereus sensu stricto (118 isolates) and Bacillus thuringiensis (62 isolates). The safety of Gergoush was evaluated based on the counts and toxin gene profiles of the dominant B. cereus species. Considering that no bacteria survived the baking process, and that the cereulide synthetase gene cesB involved in the production of the heat stable emetic toxin cereulide was not detected in any of the investigated B. cereus isolates, the results indicate, that Gergoush produced at the traditional production site is safe for human consumption. This study is the first to identify the Bacillus of Gergoush to species level, and it is the first to perform a safety evaluation of the product, based on the dominant B. cereus species.     

Microbiological quality of Brazilian UHT milk: Identification and spoilage potential of spore‐forming bacteria

Counts of aerobic mesophilic micro‐organisms and aerobic mesophilic spore‐forming bacteria were determined in 91 ultra‐high‐temperature (UHT) commercial Brazilian samples. Forty‐six spore‐forming bacteria were identified and characterised in terms of their spoilage potential. Among the 20 brands evaluated, 45% had counts of aerobic mesophilic micro‐organisms higher than 1.0 × 102 cfu/mL. The sporulated bacteria were identified as Bacillus subtilis/amyloliquefaciens, Bacillus licheniformis, Bacillus pumilus and Bacillus megaterium, and 31% and 33% showed proteolytic and lipolytic activity, respectively. Our findings indicate that there is a potential risk of UHT milk samples becoming spoiled during their commercial shelf life.     

Prevalence,antimicrobial susceptibility,and antibiotic resistance gene transfer of Bacillus strains isolated from pasteurized milk

Pasteurization is carried out in dairy industries to kill harmful bacteria present in raw milk. However, endospore-forming bacteria, such as Bacillus, cannot be completely eliminated by pasteurization. In this study, a total of 114 Bacillus strains were isolated from 133 pasteurized milk samples. Antibiotic susceptibility tests showed that the percentage of Bacillus with intrinsic resistance to ampicillin and penicillin were 80 and 86%, respectively. Meanwhile, some Bacillus isolates had acquired resistance, including trimethoprim-sulfamethoxazole resistance (10 isolates), clindamycin resistance (8 isolates), erythromycin resistance (2 isolates), and tetracycline resistance (1 isolate). To further locate these acquired resistance genes, the plasmids were investigated in these 16 Bacillus strains. The plasmid profile indicated that Bacillus cereus BA008, BA117, and BA119 harbored plasmids, respectively. Subsequently, the Illumina Novaseq PE150 was applied for the genomic and plasmid DNA sequencing. Notably, the gene tetL encoding tetracycline efflux protein was found to be located on plasmid pBC46-TL of B. cereus BA117. In vitro conjugative transfer indicated that pBC46-TL can be transferred into Bacillus invictae BA142, Bacillus safensis BA143, and Bacillus licheniformis BA130. The frequencies were of 1.5 × 10^?7 to 1.7 × 10^?5 transconjugants per donor cells. Therefore, Bacillus strains with acquired antibiotic resistance may represent a potential risk for the spread of antibiotic resistance between Bacillus and other clinical pathogens via horizontal gene transfer.     

A filtration-based real-time PCR method for the quantitative detection of viable Salmonella enterica and Listeria monocytogenes in food samples

We developed a novel filtration-based method that can eliminate dead or severally damaged Salmonella enterica and Listeria monocytogenes in food samples. This new method can recover all viable bacteria in less than 30 min, and can be coupled with a subsequent bacterial DNA extraction and real-time PCR. No statically significant differences (p < 0.01) were found between real-time PCR results obtained separately from S. enterica and L. monocytogenes when different ratios of living and dead cells were used. The analytical sensitivity in both cases was 1 genome equivalent (GE), and the quantification was linear (R² > 0.9969) over a 5-log dynamic range with PCR efficiencies >0.9754. When compared with the standard microbiological methods for the detection of these foodborne pathogens, the relative accuracy was excellent ranging from 95.72% to 104.48%. Finally, we applied the pre-treatment method to the direct detection of viable forms of these foodborne pathogens in food samples using yogurt as a model, the results being similar to those obtained using pure cultures.     

Use of Fourier transform infrared spectroscopy for rapid comparative analysis of Bacillus and Micrococcus isolates

The identification of foodborne microorganisms and their endospores in food products are important for food safety. The present work compares Bacillus (Bacillus licheniformis, Bacillus circulans and Bacillus subtilis) and Micrococcus (Micrococcus luteus) species with Fourier transform infrared (FTIR) spectroscopy. Our results show that there are several characteristic peaks belonging to both the Micrococcus and Bacillus species which can be used for the identification of these foodborne bacteria and their endospores. For Micrococcus species, a new band was observed at 1338 cm⁻¹ which may be due to acetate oxidation via the carboxylic acid cycle. The bands at 1313 cm⁻¹ and 1256 cm⁻¹ can be explained by an exopolymer formation and the other bands at 1074 cm⁻¹ and 550 cm⁻¹, may be due to the glycogen-like storage material in Micrococcus spp. There are also characteristic peaks at 993 cm⁻¹ and 801 cm⁻¹ for these bacterial species. Different Bacillus species also showed characteristic peaks at 1000–500 cm⁻¹ region. Dipicolinic acid (DPA) bands at ∼728 cm⁻¹ and ∼703 cm⁻¹ seen only in B. circulans were the marker of an endospore formation.     

Comparative accounts of probiotic characteristics of Bacillus spp. isolated from food wastes

Bacillus strains JHT3, DET6 and DET9 were selectively isolated from food wastes. These isolates exhibited various degrees of essential probiotic qualities and varied level of susceptibility patterns against tested antibiotics. Spores of DET9 elucidated best tolerance against simulated gastro-acidic conditions whereas DET6 showed best steadiness against simulated intestinal conditions. DET6 exhibited better antimicrobial activity than JHT3 and DET9 against unsafe organisms viz Staphylococcus aureus, Micrococcus flavus, Proteus vulgaris, Salmonella typhi and Escherichia coli. Susceptibility of these isolates to antibiotics decreases the illustration to offer resistance determinants to other organisms if administered in the form of probiotic preparations. JHT3, DET6 and DET9 showed high homology with Bacillus megaterium, (98%) Bacillus subtilis (99%) and Bacillus thuringiensis, respectively, using partial 16S r-RNA gene sequencing. Biochemical characterizations have supported the results of partial 16S r-RNA gene sequencing for JHT3 and DET6 but did not for DET9 and revealed its innovation. These isolates exhibited zero mortality of fishes in a 60 days trial, when fishes (Surfi tetra) were challenged up to 100 ppm cell concentration, with their daily diet.